Are you talking about the 'match' - or lottery after the game is played when the last 2 digits of a players score matches the number on the backglass?
A knocker sounds and a credit is added to the credit wheel ?

http://www.pinrepair.com/em/index1.htm#steps

Sounds like you will have to take apart, clean , reassemble that credit unit.
the way you described it the pulse is getting to the unit but it wont 'step up'
have you manually added credits 4-5 from inside the back box?

also is your super flight set up on free play? or do you still use the coin switch (coin door) to add a credit or start a game?

If you bring it up to say 10 games will it re set one # at a time 9-8-7 etc or does it go right to '0'?
Also before you take it apart break out the game manual for Super Flight and check all the adjustments, I have manuals for Space Mission & Big Ben both games came latter then yours but might have a few areas that are the same-
-Play Adjustment (back box) credit or extra ball
-25 cent adjustment
-1 coin-1 play 2 coin - 3 plays adjustment
check those first and see what happens

Well I would take apart and clean the credit unit ,
It seems like the Wms EMs I've worked on 80% of the time it's one of the stepper units,
I think SM has 6 ? not sure how many in SF?
Also look at the 'Change' relay and 'Game Over' relay for dirty or out of adj sw contacts .

If Wms made a game manual for super flight get it they are really worth it.
it will tell you the color code of the wire and what type of SW - M+B, NO, NC
on SM the wording goes like this-
Game over relay - E-7 OPENS IN HI-SCORE CIRCUITS AND CLOSES IN NUMBER MATCH CIRCUITS TO "CREDIT EXTRA BALL" ADJUSTMENT.

On the 1 coin- 1 play 2 coin -3 plays adjustment
some of the wording that may help?-
IN 'ON' POSITION, 10 CENT ADJUSTMENT MUST BE IN #2 POSITION & 25 CENT ADJUSTMENT MUST BE IN #6 POSITION
this may help but I'm not sure how the relay board looks like in SF the IPD doesn't have a good photo yet.

www.pleasureandpinball.se/sm/smbackboxeng.htm
Also check this guys page -he has some nice photos on Wms. EMs

whatever you do dont panic
after you put it all back together did you actuate both coils/linkage by hand?
you should be able to step up 1,2,3 with the one side and step down with the other coil on the other side 3,2,1 this is with your finger with power off (game off)

you want the unit to operate freely make sure the contacts are clean and that the stationary one is moved back slightly by the other one like they talk about in the link above.
if it feels hard to step up the unit they may be too much spring pressure
How long have you had this pin and has it been running a long time?

A few more things to check out - you probably did it already but...

1 the match unit,- in the backbox next to the credit unit.
2 game over re
3 change re (not sure if you have one)
4 Coin unit- (clean all contacts on face )area called C-8 -are the numbers match circuit, every player has it's own section like '1st player match, 2nd players match on this unit check the condition of the wires going to the coin unit.

I'm glad you got it cfroadhog,
thats one of the keys to a Wms. EM from that era -the stepper units
but make sure you get the game manual/ sch. for SF it gives you a lot of info